franciscozorrilla
commented
1 year ago Hi Li,
Please also have a look at other issues before posting a new one, it is very likely that you will find helpful discussion there. For example, you will find the answer to your problem in this solved issue #103, where another user reported the same error message as you. You probably are running a newer version of Snakemake, and you will need to downgrade to version 5.10.
Best, Francisco
Dear Dr.Franciscozorrilla, when I "bash metaGEM.sh -t crossMapSeries -j 2 --nCores 24 -m 120 -h 24" it reported error "error parsing number of cores (--cores, -c, -j): must be integer, empty, or 'all'." (base) lizhihua@lizhihua-T640:/media/lizhihua/software/metaGEM$ bash metaGEM.sh -t crossMapSeries -j 2 --nCores 24 -m 120 -h 24
================================================================================================================================= Developed by: Francisco Zorrilla, Kiran R. Patil, and Aleksej Zelezniak____ Publication: doi.org/10.1101/2020.12.31.424982/\\\\\\/\\\\\\\\/\\____/\\_
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A Snakemake-based pipeline desinged to predict metabolic interactions directly from metagenomics data using high performance computer clusters
Setting current directory to root in config.yaml file ...
Parsing Snakefile to target rule: crossMapSeries ... Number of jobs to be sumitted to cluster: 2 ... Parsing cluster_config.json to match requested number of cores: 24 ... Parsing cluster_config.json to match requested time (hours): 24 ... Parsing cluster_config.json to match requested memory: 120 ...
Do you wish to continue with these parameters? (y/n)y Proceeding with crossMapSeries job(s) ...
Please verify parameters set in the config.yaml file:
path: root: /media/lizhihua/software/metaGEM scratch: /media/lizhihua/software/metaGEM_tem folder: data: dataset logs: logs assemblies: assemblies scripts: scripts crossMap: crossMap concoct: concoct maxbin: maxbin metabat: metabat refined: refined_bins reassembled: reassembled_bins classification: GTDBTk abundance: abundance GRiD: GRiD GEMs: GEMs SMETANA: SMETANA memote: memote qfiltered: qfiltered stats: stats proteinBins: protein_bins dnaBins: dna_bins pangenome: pangenome kallisto: kallisto kallistoIndex: kallistoIndex benchmarks: benchmarks prodigal: prodigal blastp: blastp blastp_db: scripts: kallisto2concoct: kallisto2concoct.py prepRoary: prepareRoaryInput.R binFilter: binFilter.py qfilterVis: qfilterVis.R assemblyVis: assemblyVis.R binningVis: binningVis.R modelVis: modelVis.R compositionVis: compositionVis.R taxonomyVis: taxonomyVis.R carveme: media_db.tsv toy: download_toydata.txt GTDBtkVis: cores: fastp: 4 megahit: 48 crossMap: 48 concoct: 48 metabat: 48 maxbin: 48 refine: 48 reassemble: 48 classify: 2 gtdbtk: 48 abundance: 16 carveme: 4 smetana: 12 memote: 4 grid: 24 prokka: 2 roary: 12 diamond: 12 params: cutfasta: 10000 assemblyPreset: meta-sensitive assemblyMin: 1000 concoct: 800 metabatMin: 50000 seed: 420 minBin: 1500 refineMem: 1600 refineComp: 50 refineCont: 10 reassembleMem: 1600 reassembleComp: 50 reassembleCont: 10 carveMedia: M8 smetanaMedia: M1,M2,M3,M4,M5,M7,M8,M9,M10,M11,M13,M14,M15A,M15B,M16 smetanaSolver: CPLEX roaryI: 90 roaryCD: 90 envs: metagem: /media/lizhihua/software/metaGEM/envs/metagem metawrap: /media/lizhihua/software/metaGEM/envs/metawrap prokkaroary: /media/lizhihua/software/metaGEM/envs/prokkaroary
Please pay close attention to make sure that your paths are properly configured! Do you wish to proceed with this config.yaml file? (y/n)y
Please verify parameters set in the cluster_config.json file:
{ "default" : { "account" : "LZLJ", "time" : "0-24:00:00", "n" : 24, "tasks" : 1, "mem" : 120G, "name" : "DL.{rule}", "output" : "logs/{wildcards}.%N.{rule}.out.log", },
Do you wish to proceed with this cluster_config.json file? (y/n)y
Unlocking snakemake ... /home/lizhihua/miniconda3/lib/python3.8/site-packages/requests/init.py:89: RequestsDependencyWarning: urllib3 (1.25.11) or chardet (5.0.0) doesn't match a supported version! warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported " Unlocking working directory.
Dry-running snakemake jobs ... Error parsing number of cores (--cores, -c, -j): must be integer, empty, or 'all'. Do you wish to submit this batch of jobs? (y/n)y nohup: appending output to 'nohup.out' (base) lizhihua@lizhihua-T640:/media/lizhihua/software/metaGEM$